Multiple sequence alignment - TraesCS2A01G457100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G457100 chr2A 100.000 4530 0 0 1 4530 705739150 705743679 0.000000e+00 8366.0
1 TraesCS2A01G457100 chr2D 91.698 2891 127 36 834 3640 565153719 565156580 0.000000e+00 3904.0
2 TraesCS2A01G457100 chr2D 92.275 466 32 4 185 648 565152747 565153210 0.000000e+00 658.0
3 TraesCS2A01G457100 chr2D 91.275 447 35 2 3052 3497 570134248 570134691 1.390000e-169 606.0
4 TraesCS2A01G457100 chr2D 78.500 1093 104 61 3498 4530 570135049 570136070 3.020000e-166 595.0
5 TraesCS2A01G457100 chr2D 90.152 264 18 4 4230 4493 565157342 565157597 2.020000e-88 337.0
6 TraesCS2A01G457100 chr2D 86.486 111 4 2 638 737 565153230 565153340 1.330000e-20 111.0
7 TraesCS2A01G457100 chr2D 93.023 43 3 0 798 840 441833874 441833916 3.780000e-06 63.9
8 TraesCS2A01G457100 chr2B 88.975 2712 196 53 1561 4226 677021326 677023980 0.000000e+00 3256.0
9 TraesCS2A01G457100 chr2B 87.969 640 34 18 836 1452 677020446 677021065 0.000000e+00 715.0
10 TraesCS2A01G457100 chr2B 92.359 301 15 4 4230 4530 677024011 677024303 5.420000e-114 422.0
11 TraesCS2A01G457100 chr2B 84.514 381 51 6 254 630 677018777 677019153 1.990000e-98 370.0
12 TraesCS2A01G457100 chr2B 86.364 66 6 3 774 836 117900338 117900403 8.130000e-08 69.4
13 TraesCS2A01G457100 chr6A 97.382 191 4 1 1 190 614646576 614646766 1.570000e-84 324.0
14 TraesCS2A01G457100 chr7A 97.368 190 4 1 1 189 730827167 730826978 5.650000e-84 322.0
15 TraesCS2A01G457100 chr7A 97.340 188 5 0 1 188 672041194 672041381 2.030000e-83 320.0
16 TraesCS2A01G457100 chr7A 96.791 187 6 0 1 187 231238757 231238943 3.400000e-81 313.0
17 TraesCS2A01G457100 chr7A 96.791 187 5 1 1 187 75247269 75247454 1.220000e-80 311.0
18 TraesCS2A01G457100 chr7A 88.000 50 5 1 798 846 660558649 660558600 1.760000e-04 58.4
19 TraesCS2A01G457100 chr3A 97.312 186 5 0 1 186 399898251 399898436 2.630000e-82 316.0
20 TraesCS2A01G457100 chr4A 97.283 184 5 0 3 186 376675362 376675179 3.400000e-81 313.0
21 TraesCS2A01G457100 chr5A 96.296 189 7 0 1 189 429967661 429967473 1.220000e-80 311.0
22 TraesCS2A01G457100 chr1A 96.774 186 6 0 1 186 538889651 538889836 1.220000e-80 311.0
23 TraesCS2A01G457100 chr3D 84.932 73 3 3 775 839 455048103 455048031 2.920000e-07 67.6
24 TraesCS2A01G457100 chr1D 95.122 41 2 0 798 838 462295103 462295143 1.050000e-06 65.8
25 TraesCS2A01G457100 chr1D 89.583 48 4 1 798 845 375980874 375980920 4.890000e-05 60.2
26 TraesCS2A01G457100 chr3B 91.489 47 3 1 793 838 2998676 2998630 3.780000e-06 63.9
27 TraesCS2A01G457100 chr3B 92.857 42 3 0 798 839 71975525 71975484 1.360000e-05 62.1
28 TraesCS2A01G457100 chr4B 89.130 46 5 0 798 843 568664771 568664726 1.760000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G457100 chr2A 705739150 705743679 4529 False 8366.00 8366 100.00000 1 4530 1 chr2A.!!$F1 4529
1 TraesCS2A01G457100 chr2D 565152747 565157597 4850 False 1252.50 3904 90.15275 185 4493 4 chr2D.!!$F2 4308
2 TraesCS2A01G457100 chr2D 570134248 570136070 1822 False 600.50 606 84.88750 3052 4530 2 chr2D.!!$F3 1478
3 TraesCS2A01G457100 chr2B 677018777 677024303 5526 False 1190.75 3256 88.45425 254 4530 4 chr2B.!!$F2 4276

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
844 1948 0.837272 GGCCAGGTATACTTGAGCCA 59.163 55.000 27.52 0.0 38.34 4.75 F
1396 2524 0.108329 CCGTATCTTCAGGCAACGGT 60.108 55.000 4.12 0.0 46.10 4.83 F
1401 2529 0.468226 TCTTCAGGCAACGGTTCAGT 59.532 50.000 0.00 0.0 46.39 3.41 F
3269 4611 1.225704 GAGTTGGATGGGAGGCTGG 59.774 63.158 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 3492 2.026729 TGTGGGATGGAGCAAACGATAA 60.027 45.455 0.0 0.0 0.00 1.75 R
3370 4712 0.107848 GGGTACAATCCAGGTCCACG 60.108 60.000 0.0 0.0 0.00 4.94 R
3402 4744 1.941294 GAGATCGCAGGAGTCGAACTA 59.059 52.381 0.0 0.0 38.80 2.24 R
4226 6138 0.033090 GAACGGGACCAAGTCGAACT 59.967 55.000 0.0 0.0 32.65 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 7.591006 TCTATAAGCTTGGTCAAACTTTACG 57.409 36.000 9.86 0.00 0.00 3.18
132 133 7.380536 TCTATAAGCTTGGTCAAACTTTACGA 58.619 34.615 9.86 0.00 0.00 3.43
133 134 6.870971 ATAAGCTTGGTCAAACTTTACGAA 57.129 33.333 9.86 0.00 0.00 3.85
134 135 4.813296 AGCTTGGTCAAACTTTACGAAG 57.187 40.909 0.00 0.00 38.87 3.79
161 162 6.503616 GACTTCAGTCAACTCTAATATGCG 57.496 41.667 1.86 0.00 44.18 4.73
162 163 5.352284 ACTTCAGTCAACTCTAATATGCGG 58.648 41.667 0.00 0.00 0.00 5.69
163 164 5.127194 ACTTCAGTCAACTCTAATATGCGGA 59.873 40.000 0.00 0.00 0.00 5.54
164 165 5.188327 TCAGTCAACTCTAATATGCGGAG 57.812 43.478 0.00 0.00 0.00 4.63
165 166 4.645136 TCAGTCAACTCTAATATGCGGAGT 59.355 41.667 0.00 0.00 41.37 3.85
166 167 5.826208 TCAGTCAACTCTAATATGCGGAGTA 59.174 40.000 6.10 0.00 39.09 2.59
167 168 6.320418 TCAGTCAACTCTAATATGCGGAGTAA 59.680 38.462 6.10 0.00 39.09 2.24
168 169 6.978659 CAGTCAACTCTAATATGCGGAGTAAA 59.021 38.462 6.10 0.00 39.09 2.01
169 170 7.653713 CAGTCAACTCTAATATGCGGAGTAAAT 59.346 37.037 6.10 0.00 39.09 1.40
170 171 8.857098 AGTCAACTCTAATATGCGGAGTAAATA 58.143 33.333 6.10 0.00 39.09 1.40
171 172 9.472361 GTCAACTCTAATATGCGGAGTAAATAA 57.528 33.333 6.10 0.00 39.09 1.40
176 177 9.793245 CTCTAATATGCGGAGTAAATAAAAACG 57.207 33.333 0.00 0.00 0.00 3.60
177 178 8.767085 TCTAATATGCGGAGTAAATAAAAACGG 58.233 33.333 0.00 0.00 0.00 4.44
178 179 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
179 180 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
180 181 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
181 182 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
182 183 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
183 184 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
184 185 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
185 186 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
186 187 7.278135 GGAGTAAATAAAAACGGAGGGAGTAT 58.722 38.462 0.00 0.00 0.00 2.12
187 188 7.772292 GGAGTAAATAAAAACGGAGGGAGTATT 59.228 37.037 0.00 0.00 0.00 1.89
188 189 8.728337 AGTAAATAAAAACGGAGGGAGTATTC 57.272 34.615 0.00 0.00 0.00 1.75
189 190 8.323567 AGTAAATAAAAACGGAGGGAGTATTCA 58.676 33.333 0.00 0.00 0.00 2.57
190 191 8.949177 GTAAATAAAAACGGAGGGAGTATTCAA 58.051 33.333 0.00 0.00 0.00 2.69
191 192 6.997239 ATAAAAACGGAGGGAGTATTCAAC 57.003 37.500 0.00 0.00 0.00 3.18
192 193 4.635699 AAAACGGAGGGAGTATTCAACT 57.364 40.909 0.00 0.00 42.80 3.16
193 194 4.635699 AAACGGAGGGAGTATTCAACTT 57.364 40.909 0.00 0.00 39.07 2.66
194 195 4.635699 AACGGAGGGAGTATTCAACTTT 57.364 40.909 0.00 0.00 39.07 2.66
195 196 4.635699 ACGGAGGGAGTATTCAACTTTT 57.364 40.909 0.00 0.00 39.07 2.27
196 197 4.576879 ACGGAGGGAGTATTCAACTTTTC 58.423 43.478 0.00 0.00 39.07 2.29
197 198 3.939592 CGGAGGGAGTATTCAACTTTTCC 59.060 47.826 0.00 0.00 39.07 3.13
198 199 3.939592 GGAGGGAGTATTCAACTTTTCCG 59.060 47.826 0.00 0.00 39.07 4.30
199 200 4.565028 GGAGGGAGTATTCAACTTTTCCGT 60.565 45.833 0.00 0.00 39.07 4.69
205 206 6.817140 GGAGTATTCAACTTTTCCGTGATAGT 59.183 38.462 0.00 0.00 39.07 2.12
217 218 6.844696 TTCCGTGATAGTCTGCAAATAATC 57.155 37.500 0.00 0.00 0.00 1.75
225 226 3.753272 AGTCTGCAAATAATCGCACTGTT 59.247 39.130 0.00 0.00 33.75 3.16
226 227 4.216257 AGTCTGCAAATAATCGCACTGTTT 59.784 37.500 0.00 0.00 33.75 2.83
238 239 5.570262 TCGCACTGTTTATTATCATACGC 57.430 39.130 0.00 0.00 0.00 4.42
270 271 7.864882 TCATATCTATCTTCAAAGCAGAACTCG 59.135 37.037 0.00 0.00 0.00 4.18
293 294 6.592607 TCGTGTTCTTCTTCGGCTTATTTATT 59.407 34.615 0.00 0.00 0.00 1.40
353 354 6.985188 TTGTTGATGATAAGTCTACCAAGC 57.015 37.500 0.00 0.00 0.00 4.01
369 370 3.119849 ACCAAGCACGAAAGCATATTGTC 60.120 43.478 0.00 0.00 36.85 3.18
391 392 5.182380 GTCCCAACAAAATAACATCCGAGAA 59.818 40.000 0.00 0.00 0.00 2.87
408 409 4.806247 CCGAGAACACTAATTTGAGCCTAG 59.194 45.833 0.00 0.00 0.00 3.02
546 551 6.138263 TGATGGCCTCCATATCATTTTCTTT 58.862 36.000 3.32 0.00 45.26 2.52
597 602 1.330155 TCCTCTCCATAAGGACCCCT 58.670 55.000 0.00 0.00 39.61 4.79
650 686 9.574516 AAAATCTATCCGGATAGCACTTTTTAT 57.425 29.630 36.77 23.43 40.37 1.40
675 713 1.794116 TGACGCGTAAGGCTTTGTTAC 59.206 47.619 13.97 0.00 40.44 2.50
693 731 8.942669 TTTGTTACGTCAACATTTATCATGTC 57.057 30.769 0.00 0.00 46.38 3.06
694 732 7.659652 TGTTACGTCAACATTTATCATGTCA 57.340 32.000 0.00 0.00 42.29 3.58
696 734 8.726068 TGTTACGTCAACATTTATCATGTCATT 58.274 29.630 0.00 0.00 42.29 2.57
737 786 4.501229 GCAACAAATCAAGGTCATCCAACA 60.501 41.667 0.00 0.00 35.89 3.33
738 787 5.786311 CAACAAATCAAGGTCATCCAACAT 58.214 37.500 0.00 0.00 35.89 2.71
739 788 6.225318 CAACAAATCAAGGTCATCCAACATT 58.775 36.000 0.00 0.00 35.89 2.71
741 790 7.537596 ACAAATCAAGGTCATCCAACATTTA 57.462 32.000 0.00 0.00 35.89 1.40
743 792 8.253113 ACAAATCAAGGTCATCCAACATTTATC 58.747 33.333 0.00 0.00 35.89 1.75
748 797 6.949352 AGGTCATCCAACATTTATCATGTC 57.051 37.500 0.00 0.00 35.89 3.06
749 798 6.425735 AGGTCATCCAACATTTATCATGTCA 58.574 36.000 0.00 0.00 35.89 3.58
750 799 7.064866 AGGTCATCCAACATTTATCATGTCAT 58.935 34.615 0.00 0.00 35.89 3.06
752 801 8.199449 GGTCATCCAACATTTATCATGTCATTT 58.801 33.333 0.00 0.00 0.00 2.32
778 827 5.998454 ATAGTGCAGAATTTTCTCGATGG 57.002 39.130 0.00 0.00 34.74 3.51
779 828 2.421424 AGTGCAGAATTTTCTCGATGGC 59.579 45.455 0.00 0.00 34.74 4.40
782 831 2.789092 GCAGAATTTTCTCGATGGCACG 60.789 50.000 0.00 0.00 34.74 5.34
784 833 1.398390 GAATTTTCTCGATGGCACGCT 59.602 47.619 0.00 0.00 0.00 5.07
785 834 1.009829 ATTTTCTCGATGGCACGCTC 58.990 50.000 0.00 0.00 0.00 5.03
786 835 1.351430 TTTTCTCGATGGCACGCTCG 61.351 55.000 2.67 2.67 37.44 5.03
787 836 3.699955 TTCTCGATGGCACGCTCGG 62.700 63.158 8.90 1.20 36.87 4.63
844 1948 0.837272 GGCCAGGTATACTTGAGCCA 59.163 55.000 27.52 0.00 38.34 4.75
906 2010 1.337167 GCATGGCCAGGAAAAGAACAC 60.337 52.381 24.18 0.00 0.00 3.32
952 2056 2.751436 CCCATGCCACCAACCGAG 60.751 66.667 0.00 0.00 0.00 4.63
953 2057 2.350895 CCATGCCACCAACCGAGA 59.649 61.111 0.00 0.00 0.00 4.04
954 2058 1.303236 CCATGCCACCAACCGAGAA 60.303 57.895 0.00 0.00 0.00 2.87
956 2060 1.671054 ATGCCACCAACCGAGAACG 60.671 57.895 0.00 0.00 39.43 3.95
957 2061 3.723348 GCCACCAACCGAGAACGC 61.723 66.667 0.00 0.00 38.29 4.84
958 2062 2.030562 CCACCAACCGAGAACGCT 59.969 61.111 0.00 0.00 38.29 5.07
959 2063 1.597027 CCACCAACCGAGAACGCTT 60.597 57.895 0.00 0.00 38.29 4.68
962 2066 2.380410 CCAACCGAGAACGCTTCCG 61.380 63.158 0.00 0.00 38.29 4.30
1124 2252 4.823419 TGACGCGGGCGGGTAATG 62.823 66.667 18.03 0.00 44.69 1.90
1181 2309 0.183971 GATCTCTCGGGTCCTCCTCA 59.816 60.000 0.00 0.00 0.00 3.86
1182 2310 0.856982 ATCTCTCGGGTCCTCCTCAT 59.143 55.000 0.00 0.00 0.00 2.90
1183 2311 0.631753 TCTCTCGGGTCCTCCTCATT 59.368 55.000 0.00 0.00 0.00 2.57
1203 2331 7.095439 CCTCATTATAGCTCACGGATTTTCTTC 60.095 40.741 0.00 0.00 0.00 2.87
1313 2441 4.891727 GACCGCGTCATGGCCGAT 62.892 66.667 4.92 0.00 32.09 4.18
1361 2489 4.292178 CATCGCCCTCGCCTCTCC 62.292 72.222 0.00 0.00 35.26 3.71
1396 2524 0.108329 CCGTATCTTCAGGCAACGGT 60.108 55.000 4.12 0.00 46.10 4.83
1397 2525 1.674817 CCGTATCTTCAGGCAACGGTT 60.675 52.381 4.12 0.00 46.10 4.44
1398 2526 1.659098 CGTATCTTCAGGCAACGGTTC 59.341 52.381 0.00 0.00 46.39 3.62
1399 2527 2.695359 GTATCTTCAGGCAACGGTTCA 58.305 47.619 0.00 0.00 46.39 3.18
1400 2528 1.813513 ATCTTCAGGCAACGGTTCAG 58.186 50.000 0.00 0.00 46.39 3.02
1401 2529 0.468226 TCTTCAGGCAACGGTTCAGT 59.532 50.000 0.00 0.00 46.39 3.41
1405 2541 2.096248 TCAGGCAACGGTTCAGTTTTT 58.904 42.857 0.00 0.00 46.39 1.94
1409 2545 3.634910 AGGCAACGGTTCAGTTTTTATGT 59.365 39.130 0.00 0.00 46.39 2.29
1496 2766 4.018415 AGGAGTACAATGCTTATGGTGGTT 60.018 41.667 0.00 0.00 0.00 3.67
1497 2767 5.190925 AGGAGTACAATGCTTATGGTGGTTA 59.809 40.000 0.00 0.00 0.00 2.85
1498 2768 6.062095 GGAGTACAATGCTTATGGTGGTTAT 58.938 40.000 0.00 0.00 0.00 1.89
1535 2818 6.751514 TTGCAAAAGCTTCGATAGGATTTA 57.248 33.333 0.00 0.00 0.00 1.40
1538 2821 6.318648 TGCAAAAGCTTCGATAGGATTTATGT 59.681 34.615 0.00 0.00 0.00 2.29
1539 2822 7.148086 TGCAAAAGCTTCGATAGGATTTATGTT 60.148 33.333 0.00 0.00 0.00 2.71
1543 2826 6.591935 AGCTTCGATAGGATTTATGTTGGAA 58.408 36.000 0.00 0.00 0.00 3.53
1546 2829 7.519008 GCTTCGATAGGATTTATGTTGGAACAG 60.519 40.741 0.00 0.00 43.04 3.16
1559 2859 9.967451 TTATGTTGGAACAGATTTAACCATCTA 57.033 29.630 0.00 0.00 43.04 1.98
1675 2994 3.119137 ACTGCAGGAGTTTGTTTTTCCAC 60.119 43.478 19.93 0.00 33.32 4.02
1676 2995 3.096092 TGCAGGAGTTTGTTTTTCCACT 58.904 40.909 0.00 0.00 33.32 4.00
1684 3003 4.929211 AGTTTGTTTTTCCACTCAGTTTGC 59.071 37.500 0.00 0.00 0.00 3.68
1752 3084 6.978674 AAATCCGACAGTTATCAGGAGATA 57.021 37.500 0.00 0.00 35.67 1.98
1761 3093 8.560124 ACAGTTATCAGGAGATAGAAAATCCT 57.440 34.615 0.00 0.00 44.41 3.24
1762 3094 8.646900 ACAGTTATCAGGAGATAGAAAATCCTC 58.353 37.037 0.00 0.00 41.60 3.71
1763 3095 8.093927 CAGTTATCAGGAGATAGAAAATCCTCC 58.906 40.741 0.00 0.00 41.60 4.30
1764 3096 7.236640 AGTTATCAGGAGATAGAAAATCCTCCC 59.763 40.741 0.00 0.00 44.72 4.30
1767 3099 6.634041 TCAGGAGATAGAAAATCCTCCCATA 58.366 40.000 0.00 0.00 44.72 2.74
1793 3125 2.268730 GCAGTTTGCTTGATGTAGGC 57.731 50.000 0.00 0.00 40.96 3.93
1803 3135 6.772360 TGCTTGATGTAGGCAAAATCAATA 57.228 33.333 8.55 1.39 38.58 1.90
1804 3136 7.350744 TGCTTGATGTAGGCAAAATCAATAT 57.649 32.000 8.55 0.00 38.58 1.28
1993 3325 5.809001 TCCTATTTGTGCTTCAACAGAGAT 58.191 37.500 0.00 0.00 35.61 2.75
2176 3508 4.695217 TTTGGTTATCGTTTGCTCCATC 57.305 40.909 0.00 0.00 0.00 3.51
2178 3510 1.947456 GGTTATCGTTTGCTCCATCCC 59.053 52.381 0.00 0.00 0.00 3.85
2180 3512 2.325583 TATCGTTTGCTCCATCCCAC 57.674 50.000 0.00 0.00 0.00 4.61
2184 3516 1.339610 CGTTTGCTCCATCCCACAAAA 59.660 47.619 0.00 0.00 34.10 2.44
2210 3542 6.925165 ACATTAAATGGTTTCTGCTTTGACTG 59.075 34.615 0.00 0.00 33.60 3.51
2238 3570 2.358582 TGATGATGCTATTTGGGTTGCG 59.641 45.455 0.00 0.00 0.00 4.85
2281 3613 2.500910 AGATCTGAGTGGGAAGAAGCAG 59.499 50.000 0.00 0.00 0.00 4.24
2407 3741 7.166691 AGCTCAATTTATGTCAGCATTCTTT 57.833 32.000 0.00 0.00 36.58 2.52
2421 3755 9.284594 GTCAGCATTCTTTTTATTTTATACGCA 57.715 29.630 0.00 0.00 0.00 5.24
2425 3759 8.325282 GCATTCTTTTTATTTTATACGCAACCC 58.675 33.333 0.00 0.00 0.00 4.11
2428 3762 9.984190 TTCTTTTTATTTTATACGCAACCCTTT 57.016 25.926 0.00 0.00 0.00 3.11
2433 3767 6.827586 ATTTTATACGCAACCCTTTTCAGA 57.172 33.333 0.00 0.00 0.00 3.27
2434 3768 6.636562 TTTTATACGCAACCCTTTTCAGAA 57.363 33.333 0.00 0.00 0.00 3.02
2445 3780 8.335356 GCAACCCTTTTCAGAATTTTTAAGTTC 58.665 33.333 0.00 0.00 0.00 3.01
2460 3795 9.899226 ATTTTTAAGTTCTTGTGTAGAATCAGC 57.101 29.630 0.00 0.00 44.39 4.26
2461 3796 6.706055 TTAAGTTCTTGTGTAGAATCAGCG 57.294 37.500 0.00 0.00 44.39 5.18
2462 3797 4.521130 AGTTCTTGTGTAGAATCAGCGA 57.479 40.909 0.00 0.00 44.39 4.93
2463 3798 5.078411 AGTTCTTGTGTAGAATCAGCGAT 57.922 39.130 0.00 0.00 44.39 4.58
2464 3799 5.482908 AGTTCTTGTGTAGAATCAGCGATT 58.517 37.500 3.90 3.90 44.39 3.34
2465 3800 5.578727 AGTTCTTGTGTAGAATCAGCGATTC 59.421 40.000 17.85 17.85 46.05 2.52
2614 3949 1.268899 GATGATGCTGGTTGCCTATGC 59.731 52.381 0.00 0.00 42.00 3.14
2617 3952 2.044053 GCTGGTTGCCTATGCCCA 60.044 61.111 0.00 0.00 36.33 5.36
2983 4325 2.265589 TTCTTTTGGACGAGAACCCC 57.734 50.000 0.00 0.00 0.00 4.95
3129 4471 1.541670 GGCAACTCCTACAAACCGTCA 60.542 52.381 0.00 0.00 0.00 4.35
3146 4488 4.124238 CCGTCAAAAGTCCTTTAGTCACA 58.876 43.478 0.00 0.00 31.63 3.58
3269 4611 1.225704 GAGTTGGATGGGAGGCTGG 59.774 63.158 0.00 0.00 0.00 4.85
3334 4676 3.825328 AGATGTGGAGCAGTCAAGTTTT 58.175 40.909 0.00 0.00 0.00 2.43
3370 4712 1.287425 CGTTTCTCCGGTTCCATAGC 58.713 55.000 0.00 0.00 0.00 2.97
3402 4744 1.656587 TGTACCCACAATCAGCTCCT 58.343 50.000 0.00 0.00 0.00 3.69
3448 4790 1.728490 GATGGGAATTGGCTGTCCGC 61.728 60.000 0.00 0.00 34.47 5.54
3540 5239 7.009907 GCTTTCCTTGCAATGAGATTAACAATC 59.990 37.037 0.00 0.00 38.20 2.67
3610 5320 5.179368 CAGAATTCTCAAAAAGCACGAGGTA 59.821 40.000 4.57 0.00 0.00 3.08
3611 5321 5.940470 AGAATTCTCAAAAAGCACGAGGTAT 59.060 36.000 0.88 0.00 0.00 2.73
3612 5322 5.803020 ATTCTCAAAAAGCACGAGGTATC 57.197 39.130 0.00 0.00 0.00 2.24
3660 5427 2.482664 CGGCTGATGTAACTGCTCTCAT 60.483 50.000 0.00 0.00 35.59 2.90
3681 5448 4.693532 CAGGCGGTACTGCTGAAA 57.306 55.556 25.32 0.00 34.52 2.69
3689 5456 2.159627 CGGTACTGCTGAAATGTTCCAC 59.840 50.000 0.00 0.00 0.00 4.02
3711 5478 5.504755 CACGTTAAGAAATCAAAGATGACGC 59.495 40.000 0.00 0.00 38.69 5.19
3840 5695 3.959573 GCTGCTGCAAGATAGGTTAAG 57.040 47.619 11.11 0.00 39.41 1.85
3841 5696 3.535561 GCTGCTGCAAGATAGGTTAAGA 58.464 45.455 11.11 0.00 39.41 2.10
3842 5697 3.941483 GCTGCTGCAAGATAGGTTAAGAA 59.059 43.478 11.11 0.00 39.41 2.52
3843 5698 4.396166 GCTGCTGCAAGATAGGTTAAGAAA 59.604 41.667 11.11 0.00 39.41 2.52
3896 5754 5.917545 AGGTGGTAGGAAGAAAGGTAAAA 57.082 39.130 0.00 0.00 0.00 1.52
3910 5768 7.593825 AGAAAGGTAAAATTTCATTCAGACCG 58.406 34.615 0.00 0.00 38.79 4.79
3913 5771 4.157840 GGTAAAATTTCATTCAGACCGCCT 59.842 41.667 0.00 0.00 0.00 5.52
3918 5776 3.459232 TTCATTCAGACCGCCTAGATG 57.541 47.619 0.00 0.00 0.00 2.90
3942 5800 7.233632 TGATTACTCCCTCCATTCCATAATTG 58.766 38.462 0.00 0.00 0.00 2.32
3966 5848 1.683943 TATGGAACGGGGAGAGTACG 58.316 55.000 0.00 0.00 0.00 3.67
3967 5849 0.324091 ATGGAACGGGGAGAGTACGT 60.324 55.000 0.00 0.00 43.43 3.57
3968 5850 0.962356 TGGAACGGGGAGAGTACGTC 60.962 60.000 0.00 0.00 40.31 4.34
3969 5851 0.679321 GGAACGGGGAGAGTACGTCT 60.679 60.000 0.00 0.00 40.31 4.18
3970 5852 1.172175 GAACGGGGAGAGTACGTCTT 58.828 55.000 0.00 0.00 40.31 3.01
3971 5853 2.359900 GAACGGGGAGAGTACGTCTTA 58.640 52.381 0.00 0.00 40.31 2.10
3972 5854 2.496899 ACGGGGAGAGTACGTCTTAA 57.503 50.000 0.00 0.00 35.77 1.85
3973 5855 2.363683 ACGGGGAGAGTACGTCTTAAG 58.636 52.381 0.00 0.00 35.77 1.85
3984 5866 5.892568 AGTACGTCTTAAGATAGGTGCTTG 58.107 41.667 8.75 0.00 0.00 4.01
4013 5895 9.757227 ATTGTTCGATGAAAAATAACCAAAGAA 57.243 25.926 0.00 0.00 28.81 2.52
4061 5965 8.027189 GTCACTGGCATACATAATCGATAGTAA 58.973 37.037 0.00 0.00 37.40 2.24
4086 5992 4.389077 CCTAACACAAGCAGTAGTAGTTGC 59.611 45.833 0.00 0.00 40.57 4.17
4122 6028 3.818961 AGTTGCATGATCACGAAACAG 57.181 42.857 14.80 0.00 0.00 3.16
4124 6030 3.058708 AGTTGCATGATCACGAAACAGTG 60.059 43.478 14.80 0.01 43.11 3.66
4130 6036 5.374080 CATGATCACGAAACAGTGTTGTAC 58.626 41.667 9.79 3.86 42.40 2.90
4131 6037 3.487942 TGATCACGAAACAGTGTTGTACG 59.512 43.478 20.67 20.67 42.40 3.67
4132 6038 2.878580 TCACGAAACAGTGTTGTACGT 58.121 42.857 21.61 21.61 44.74 3.57
4133 6039 4.026293 TCACGAAACAGTGTTGTACGTA 57.974 40.909 24.52 15.54 43.31 3.57
4149 6055 6.299023 TGTACGTAGAAGTTTTACGAGACA 57.701 37.500 27.00 24.21 44.91 3.41
4168 6074 3.123620 GCAAGCCTCGAGCAGGTG 61.124 66.667 6.99 3.15 45.61 4.00
4221 6133 0.035439 CGGTGGCAGTTTATGGACCT 60.035 55.000 0.00 0.00 0.00 3.85
4226 6138 3.055385 GTGGCAGTTTATGGACCTGACTA 60.055 47.826 0.00 0.00 0.00 2.59
4237 6176 2.094649 GGACCTGACTAGTTCGACTTGG 60.095 54.545 0.00 0.00 0.00 3.61
4386 6325 8.555361 GCACAAGAACAAATTAAGCCATTTAAA 58.445 29.630 0.00 0.00 35.03 1.52
4388 6327 9.051679 ACAAGAACAAATTAAGCCATTTAAACC 57.948 29.630 0.00 0.00 35.03 3.27
4400 6339 0.669077 TTTAAACCGGTGCATTGCGT 59.331 45.000 8.52 0.00 0.00 5.24
4452 6391 7.571919 ACCCTACTAAGCTTAGGAAAAATACC 58.428 38.462 31.67 0.00 38.84 2.73
4519 6458 3.581755 GGTCAACGCACTGACATTACTA 58.418 45.455 15.05 0.00 46.31 1.82
4520 6459 3.367025 GGTCAACGCACTGACATTACTAC 59.633 47.826 15.05 0.00 46.31 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 8.500773 CGTAAAGTTTGACCAAGCTTATAGAAA 58.499 33.333 11.28 0.00 40.24 2.52
106 107 7.874016 TCGTAAAGTTTGACCAAGCTTATAGAA 59.126 33.333 11.28 0.00 40.24 2.10
107 108 7.380536 TCGTAAAGTTTGACCAAGCTTATAGA 58.619 34.615 11.28 8.53 40.24 1.98
108 109 7.591006 TCGTAAAGTTTGACCAAGCTTATAG 57.409 36.000 11.28 6.81 40.24 1.31
109 110 7.658575 ACTTCGTAAAGTTTGACCAAGCTTATA 59.341 33.333 11.28 5.28 43.28 0.98
110 111 6.485648 ACTTCGTAAAGTTTGACCAAGCTTAT 59.514 34.615 11.28 0.00 43.28 1.73
111 112 5.818857 ACTTCGTAAAGTTTGACCAAGCTTA 59.181 36.000 11.28 0.00 43.28 3.09
112 113 4.638865 ACTTCGTAAAGTTTGACCAAGCTT 59.361 37.500 6.11 6.11 43.28 3.74
113 114 4.196971 ACTTCGTAAAGTTTGACCAAGCT 58.803 39.130 0.00 0.00 43.28 3.74
114 115 4.547406 ACTTCGTAAAGTTTGACCAAGC 57.453 40.909 0.00 0.00 43.28 4.01
138 139 5.460419 CCGCATATTAGAGTTGACTGAAGTC 59.540 44.000 3.41 3.41 44.97 3.01
139 140 5.127194 TCCGCATATTAGAGTTGACTGAAGT 59.873 40.000 0.00 0.00 0.00 3.01
140 141 5.592054 TCCGCATATTAGAGTTGACTGAAG 58.408 41.667 0.00 0.00 0.00 3.02
141 142 5.127194 ACTCCGCATATTAGAGTTGACTGAA 59.873 40.000 0.00 0.00 37.60 3.02
142 143 4.645136 ACTCCGCATATTAGAGTTGACTGA 59.355 41.667 0.00 0.00 37.60 3.41
143 144 4.938080 ACTCCGCATATTAGAGTTGACTG 58.062 43.478 0.00 0.00 37.60 3.51
144 145 6.710597 TTACTCCGCATATTAGAGTTGACT 57.289 37.500 4.78 0.00 41.09 3.41
145 146 7.948278 ATTTACTCCGCATATTAGAGTTGAC 57.052 36.000 4.78 0.00 41.09 3.18
150 151 9.793245 CGTTTTTATTTACTCCGCATATTAGAG 57.207 33.333 0.00 0.00 0.00 2.43
151 152 8.767085 CCGTTTTTATTTACTCCGCATATTAGA 58.233 33.333 0.00 0.00 0.00 2.10
152 153 8.767085 TCCGTTTTTATTTACTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
153 154 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
154 155 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
155 156 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
156 157 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
157 158 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
158 159 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
159 160 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
160 161 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
161 162 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
162 163 8.728337 AATACTCCCTCCGTTTTTATTTACTC 57.272 34.615 0.00 0.00 0.00 2.59
163 164 8.323567 TGAATACTCCCTCCGTTTTTATTTACT 58.676 33.333 0.00 0.00 0.00 2.24
164 165 8.496707 TGAATACTCCCTCCGTTTTTATTTAC 57.503 34.615 0.00 0.00 0.00 2.01
165 166 8.949177 GTTGAATACTCCCTCCGTTTTTATTTA 58.051 33.333 0.00 0.00 0.00 1.40
166 167 7.668469 AGTTGAATACTCCCTCCGTTTTTATTT 59.332 33.333 0.00 0.00 28.23 1.40
167 168 7.173032 AGTTGAATACTCCCTCCGTTTTTATT 58.827 34.615 0.00 0.00 28.23 1.40
168 169 6.718294 AGTTGAATACTCCCTCCGTTTTTAT 58.282 36.000 0.00 0.00 28.23 1.40
169 170 6.117975 AGTTGAATACTCCCTCCGTTTTTA 57.882 37.500 0.00 0.00 28.23 1.52
170 171 4.981812 AGTTGAATACTCCCTCCGTTTTT 58.018 39.130 0.00 0.00 28.23 1.94
171 172 4.635699 AGTTGAATACTCCCTCCGTTTT 57.364 40.909 0.00 0.00 28.23 2.43
172 173 4.635699 AAGTTGAATACTCCCTCCGTTT 57.364 40.909 0.00 0.00 35.54 3.60
173 174 4.635699 AAAGTTGAATACTCCCTCCGTT 57.364 40.909 0.00 0.00 35.54 4.44
174 175 4.565028 GGAAAAGTTGAATACTCCCTCCGT 60.565 45.833 0.00 0.00 35.54 4.69
175 176 3.939592 GGAAAAGTTGAATACTCCCTCCG 59.060 47.826 0.00 0.00 35.54 4.63
176 177 3.939592 CGGAAAAGTTGAATACTCCCTCC 59.060 47.826 0.00 0.00 35.54 4.30
177 178 4.392138 CACGGAAAAGTTGAATACTCCCTC 59.608 45.833 0.00 0.00 35.54 4.30
178 179 4.041198 TCACGGAAAAGTTGAATACTCCCT 59.959 41.667 0.00 0.00 35.54 4.20
179 180 4.320870 TCACGGAAAAGTTGAATACTCCC 58.679 43.478 0.00 0.00 35.54 4.30
180 181 6.817140 ACTATCACGGAAAAGTTGAATACTCC 59.183 38.462 0.00 0.00 35.54 3.85
181 182 7.760340 AGACTATCACGGAAAAGTTGAATACTC 59.240 37.037 0.00 0.00 35.54 2.59
182 183 7.545965 CAGACTATCACGGAAAAGTTGAATACT 59.454 37.037 0.00 0.00 39.32 2.12
183 184 7.674240 GCAGACTATCACGGAAAAGTTGAATAC 60.674 40.741 0.00 0.00 0.00 1.89
184 185 6.312918 GCAGACTATCACGGAAAAGTTGAATA 59.687 38.462 0.00 0.00 0.00 1.75
185 186 5.122396 GCAGACTATCACGGAAAAGTTGAAT 59.878 40.000 0.00 0.00 0.00 2.57
186 187 4.451096 GCAGACTATCACGGAAAAGTTGAA 59.549 41.667 0.00 0.00 0.00 2.69
187 188 3.994392 GCAGACTATCACGGAAAAGTTGA 59.006 43.478 0.00 0.00 0.00 3.18
188 189 3.745975 TGCAGACTATCACGGAAAAGTTG 59.254 43.478 0.00 0.00 0.00 3.16
189 190 4.002906 TGCAGACTATCACGGAAAAGTT 57.997 40.909 0.00 0.00 0.00 2.66
190 191 3.678056 TGCAGACTATCACGGAAAAGT 57.322 42.857 0.00 0.00 0.00 2.66
191 192 5.551760 ATTTGCAGACTATCACGGAAAAG 57.448 39.130 0.00 0.00 0.00 2.27
192 193 7.465379 CGATTATTTGCAGACTATCACGGAAAA 60.465 37.037 0.00 0.00 0.00 2.29
193 194 6.019075 CGATTATTTGCAGACTATCACGGAAA 60.019 38.462 0.00 0.00 0.00 3.13
194 195 5.462068 CGATTATTTGCAGACTATCACGGAA 59.538 40.000 0.00 0.00 0.00 4.30
195 196 4.982295 CGATTATTTGCAGACTATCACGGA 59.018 41.667 0.00 0.00 0.00 4.69
196 197 4.376413 GCGATTATTTGCAGACTATCACGG 60.376 45.833 0.00 0.00 32.00 4.94
197 198 4.209080 TGCGATTATTTGCAGACTATCACG 59.791 41.667 0.00 0.00 37.33 4.35
198 199 5.235186 AGTGCGATTATTTGCAGACTATCAC 59.765 40.000 0.00 0.00 43.00 3.06
199 200 5.234972 CAGTGCGATTATTTGCAGACTATCA 59.765 40.000 0.00 0.00 43.00 2.15
205 206 4.764679 AAACAGTGCGATTATTTGCAGA 57.235 36.364 0.00 0.00 43.00 4.26
217 218 5.576337 AGCGTATGATAATAAACAGTGCG 57.424 39.130 0.00 0.00 0.00 5.34
270 271 8.965986 AAAATAAATAAGCCGAAGAAGAACAC 57.034 30.769 0.00 0.00 0.00 3.32
293 294 5.158101 TCGAGTGTTTGCGTTTTATGAAA 57.842 34.783 0.00 0.00 0.00 2.69
332 333 5.005779 CGTGCTTGGTAGACTTATCATCAAC 59.994 44.000 0.00 0.00 0.00 3.18
349 350 3.429085 GGACAATATGCTTTCGTGCTTG 58.571 45.455 0.00 0.00 0.00 4.01
351 352 2.017049 GGGACAATATGCTTTCGTGCT 58.983 47.619 0.00 0.00 0.00 4.40
369 370 5.048364 TGTTCTCGGATGTTATTTTGTTGGG 60.048 40.000 0.00 0.00 0.00 4.12
382 383 4.034510 GGCTCAAATTAGTGTTCTCGGATG 59.965 45.833 0.00 0.00 0.00 3.51
391 392 4.469945 TGGCTACTAGGCTCAAATTAGTGT 59.530 41.667 10.75 0.00 41.96 3.55
408 409 6.456501 AGATAATGTCGAAGGTTATGGCTAC 58.543 40.000 0.00 0.00 0.00 3.58
546 551 7.676004 TCAAGTGGTACTGAGAATATTGAACA 58.324 34.615 0.00 0.00 0.00 3.18
650 686 1.248785 AAGCCTTACGCGTCAGGAGA 61.249 55.000 37.02 8.48 44.76 3.71
675 713 9.127006 TGAAAAATGACATGATAAATGTTGACG 57.873 29.630 0.00 0.00 31.52 4.35
693 731 4.248058 GCTTCAGGTTCCCATGAAAAATG 58.752 43.478 0.00 0.00 35.14 2.32
694 732 3.903090 TGCTTCAGGTTCCCATGAAAAAT 59.097 39.130 0.00 0.00 35.14 1.82
696 734 2.956132 TGCTTCAGGTTCCCATGAAAA 58.044 42.857 0.00 0.00 35.14 2.29
704 753 4.301628 CTTGATTTGTTGCTTCAGGTTCC 58.698 43.478 0.00 0.00 0.00 3.62
752 801 9.208022 CCATCGAGAAAATTCTGCACTATAATA 57.792 33.333 0.00 0.00 37.73 0.98
754 803 6.017934 GCCATCGAGAAAATTCTGCACTATAA 60.018 38.462 0.00 0.00 37.73 0.98
755 804 5.466728 GCCATCGAGAAAATTCTGCACTATA 59.533 40.000 0.00 0.00 37.73 1.31
756 805 4.274459 GCCATCGAGAAAATTCTGCACTAT 59.726 41.667 0.00 0.00 37.73 2.12
757 806 3.623060 GCCATCGAGAAAATTCTGCACTA 59.377 43.478 0.00 0.00 37.73 2.74
758 807 2.421424 GCCATCGAGAAAATTCTGCACT 59.579 45.455 0.00 0.00 37.73 4.40
759 808 2.162208 TGCCATCGAGAAAATTCTGCAC 59.838 45.455 0.00 0.00 37.73 4.57
760 809 2.162208 GTGCCATCGAGAAAATTCTGCA 59.838 45.455 0.00 1.01 37.73 4.41
761 810 2.789092 CGTGCCATCGAGAAAATTCTGC 60.789 50.000 0.00 0.00 37.73 4.26
762 811 2.789092 GCGTGCCATCGAGAAAATTCTG 60.789 50.000 0.00 0.00 37.73 3.02
764 813 1.398390 AGCGTGCCATCGAGAAAATTC 59.602 47.619 0.00 0.00 0.00 2.17
765 814 1.398390 GAGCGTGCCATCGAGAAAATT 59.602 47.619 0.00 0.00 0.00 1.82
768 817 1.805539 CGAGCGTGCCATCGAGAAA 60.806 57.895 0.00 0.00 41.40 2.52
820 869 1.774254 TCAAGTATACCTGGCCATGGG 59.226 52.381 20.97 16.10 0.00 4.00
821 870 2.811873 GCTCAAGTATACCTGGCCATGG 60.812 54.545 5.51 13.05 0.00 3.66
822 871 2.498167 GCTCAAGTATACCTGGCCATG 58.502 52.381 5.51 6.06 0.00 3.66
823 872 1.421646 GGCTCAAGTATACCTGGCCAT 59.578 52.381 20.43 0.00 35.50 4.40
824 873 0.837272 GGCTCAAGTATACCTGGCCA 59.163 55.000 20.43 4.71 35.50 5.36
825 874 0.837272 TGGCTCAAGTATACCTGGCC 59.163 55.000 19.33 19.33 35.78 5.36
826 875 2.565841 CTTGGCTCAAGTATACCTGGC 58.434 52.381 0.00 3.17 36.79 4.85
844 1948 5.425196 TGGGCCTAAATAAACGAGTACTT 57.575 39.130 4.53 0.00 0.00 2.24
906 2010 2.435437 CCTTATTGGGCTGGAAAATGGG 59.565 50.000 0.00 0.00 0.00 4.00
929 2033 1.318576 GTTGGTGGCATGGGCTATAC 58.681 55.000 0.00 0.00 40.87 1.47
1124 2252 4.355720 GGTGGGGGTTCGGGGTTC 62.356 72.222 0.00 0.00 0.00 3.62
1181 2309 8.562892 CAATGAAGAAAATCCGTGAGCTATAAT 58.437 33.333 0.00 0.00 0.00 1.28
1182 2310 7.467267 GCAATGAAGAAAATCCGTGAGCTATAA 60.467 37.037 0.00 0.00 0.00 0.98
1183 2311 6.017934 GCAATGAAGAAAATCCGTGAGCTATA 60.018 38.462 0.00 0.00 0.00 1.31
1203 2331 4.651867 CCTCCTGAGGTGGCAATG 57.348 61.111 6.67 0.00 43.61 2.82
1310 2438 0.107017 AAGCAATCCTGGGGTCATCG 60.107 55.000 0.00 0.00 0.00 3.84
1313 2441 1.691219 GGAAGCAATCCTGGGGTCA 59.309 57.895 0.00 0.00 45.56 4.02
1361 2489 2.324215 CGGCATTACCTGGATGCTG 58.676 57.895 16.97 15.03 46.92 4.41
1398 2526 9.891828 TGAGCATGTTTTAGTACATAAAAACTG 57.108 29.630 21.56 18.48 43.29 3.16
1448 2718 4.081142 GTCCCCATTTATCCCCAAAACTTG 60.081 45.833 0.00 0.00 0.00 3.16
1450 2720 3.339742 AGTCCCCATTTATCCCCAAAACT 59.660 43.478 0.00 0.00 0.00 2.66
1451 2721 3.719871 AGTCCCCATTTATCCCCAAAAC 58.280 45.455 0.00 0.00 0.00 2.43
1454 2724 3.060611 CCTAGTCCCCATTTATCCCCAA 58.939 50.000 0.00 0.00 0.00 4.12
1456 2726 2.913617 CTCCTAGTCCCCATTTATCCCC 59.086 54.545 0.00 0.00 0.00 4.81
1465 2735 2.116238 GCATTGTACTCCTAGTCCCCA 58.884 52.381 0.00 0.00 0.00 4.96
1467 2737 5.511545 CCATAAGCATTGTACTCCTAGTCCC 60.512 48.000 0.00 0.00 0.00 4.46
1496 2766 6.200665 GCTTTTGCAAATGTTTCAGTGACATA 59.799 34.615 21.89 0.00 46.58 2.29
1497 2767 5.006941 GCTTTTGCAAATGTTTCAGTGACAT 59.993 36.000 21.89 0.00 46.58 3.06
1498 2768 4.329528 GCTTTTGCAAATGTTTCAGTGACA 59.670 37.500 21.89 0.00 46.58 3.58
1535 2818 7.339466 GGTAGATGGTTAAATCTGTTCCAACAT 59.661 37.037 0.68 0.00 37.48 2.71
1538 2821 6.184789 GGGTAGATGGTTAAATCTGTTCCAA 58.815 40.000 0.68 0.00 37.48 3.53
1539 2822 5.339695 GGGGTAGATGGTTAAATCTGTTCCA 60.340 44.000 0.68 0.00 37.48 3.53
1543 2826 5.131142 CAGAGGGGTAGATGGTTAAATCTGT 59.869 44.000 0.68 0.00 37.48 3.41
1546 2829 5.367060 ACTCAGAGGGGTAGATGGTTAAATC 59.633 44.000 1.53 0.00 0.00 2.17
1559 2859 1.203364 ACCAGATTGACTCAGAGGGGT 60.203 52.381 1.53 0.00 0.00 4.95
1675 2994 4.380531 TGTACCAGAAGAAGCAAACTGAG 58.619 43.478 0.00 0.00 32.90 3.35
1676 2995 4.141711 ACTGTACCAGAAGAAGCAAACTGA 60.142 41.667 0.00 0.00 35.18 3.41
1684 3003 4.511826 GTGTCCAAACTGTACCAGAAGAAG 59.488 45.833 0.00 0.00 35.18 2.85
1752 3084 7.238514 ACTGCTACATATATGGGAGGATTTTCT 59.761 37.037 16.96 0.00 0.00 2.52
1813 3145 3.513462 GCAACATTTTTGCGGTAAACC 57.487 42.857 0.00 0.00 35.58 3.27
1829 3161 2.610374 TCGGTGAAGTTACTTGTGCAAC 59.390 45.455 0.93 0.00 37.35 4.17
1993 3325 4.702831 TCAGCCAATAAGCATACGATCAA 58.297 39.130 0.00 0.00 34.23 2.57
2160 3492 2.026729 TGTGGGATGGAGCAAACGATAA 60.027 45.455 0.00 0.00 0.00 1.75
2176 3508 7.638134 CAGAAACCATTTAATGTTTTTGTGGG 58.362 34.615 13.69 0.00 0.00 4.61
2178 3510 7.918643 AGCAGAAACCATTTAATGTTTTTGTG 58.081 30.769 15.67 15.67 32.46 3.33
2180 3512 9.224058 CAAAGCAGAAACCATTTAATGTTTTTG 57.776 29.630 2.20 9.34 0.00 2.44
2184 3516 7.439056 CAGTCAAAGCAGAAACCATTTAATGTT 59.561 33.333 4.15 0.00 0.00 2.71
2210 3542 4.037208 CCCAAATAGCATCATCAACCTGAC 59.963 45.833 0.00 0.00 0.00 3.51
2259 3591 3.703556 CTGCTTCTTCCCACTCAGATCTA 59.296 47.826 0.00 0.00 0.00 1.98
2281 3613 2.289002 CCAATTCTCTCATTAGCGGTGC 59.711 50.000 0.00 0.00 0.00 5.01
2378 3712 9.357652 GAATGCTGACATAAATTGAGCTAAAAA 57.642 29.630 0.00 0.00 34.62 1.94
2407 3741 8.794553 TCTGAAAAGGGTTGCGTATAAAATAAA 58.205 29.630 0.00 0.00 0.00 1.40
2434 3768 9.899226 GCTGATTCTACACAAGAACTTAAAAAT 57.101 29.630 0.00 0.00 46.90 1.82
2445 3780 4.260132 GCTGAATCGCTGATTCTACACAAG 60.260 45.833 22.67 15.31 45.92 3.16
2462 3797 2.687700 ATCTTGAGTCAGCGCTGAAT 57.312 45.000 39.63 38.56 41.85 2.57
2463 3798 2.462456 AATCTTGAGTCAGCGCTGAA 57.538 45.000 39.63 24.47 41.85 3.02
2464 3799 2.462456 AAATCTTGAGTCAGCGCTGA 57.538 45.000 35.30 35.30 37.24 4.26
2465 3800 2.225019 ACAAAATCTTGAGTCAGCGCTG 59.775 45.455 31.53 31.53 36.33 5.18
2466 3801 2.481952 GACAAAATCTTGAGTCAGCGCT 59.518 45.455 2.64 2.64 36.33 5.92
2467 3802 2.723010 CGACAAAATCTTGAGTCAGCGC 60.723 50.000 0.00 0.00 36.33 5.92
2468 3803 2.159787 CCGACAAAATCTTGAGTCAGCG 60.160 50.000 0.00 0.00 36.33 5.18
2835 4176 4.315803 CGTTCGGAAGGCCAGAATATTAT 58.684 43.478 5.01 0.00 32.31 1.28
2845 4186 1.070289 AGATAATCCGTTCGGAAGGCC 59.930 52.381 17.72 0.00 37.88 5.19
3040 4382 7.554959 TGGGTGAATATATAGGGAGTCTTTC 57.445 40.000 0.00 0.00 0.00 2.62
3129 4471 8.652290 AGTAGATCTTGTGACTAAAGGACTTTT 58.348 33.333 0.00 0.00 34.23 2.27
3146 4488 6.497624 AAGCATTGATCCAGAGTAGATCTT 57.502 37.500 0.00 0.00 40.69 2.40
3334 4676 1.169661 ACGCGGCAAATTCTTGTCCA 61.170 50.000 12.47 0.00 33.31 4.02
3370 4712 0.107848 GGGTACAATCCAGGTCCACG 60.108 60.000 0.00 0.00 0.00 4.94
3402 4744 1.941294 GAGATCGCAGGAGTCGAACTA 59.059 52.381 0.00 0.00 38.80 2.24
3448 4790 5.708948 GCTATCTTGTAGCTACATCTCCAG 58.291 45.833 26.54 19.56 37.56 3.86
3610 5320 6.383147 TGGAGTCTAACTAAAATCTTCCCGAT 59.617 38.462 0.00 0.00 0.00 4.18
3611 5321 5.718130 TGGAGTCTAACTAAAATCTTCCCGA 59.282 40.000 0.00 0.00 0.00 5.14
3612 5322 5.974108 TGGAGTCTAACTAAAATCTTCCCG 58.026 41.667 0.00 0.00 0.00 5.14
3624 5334 2.028130 CAGCCGAGATGGAGTCTAACT 58.972 52.381 0.00 0.00 42.00 2.24
3677 5444 7.265647 TGATTTCTTAACGTGGAACATTTCA 57.734 32.000 0.00 0.00 44.52 2.69
3681 5448 7.504924 TCTTTGATTTCTTAACGTGGAACAT 57.495 32.000 0.00 0.00 44.52 2.71
3689 5456 5.617609 TGCGTCATCTTTGATTTCTTAACG 58.382 37.500 0.00 0.00 33.56 3.18
3711 5478 5.420409 GGAGTCCTCCTAAAGTACATGTTG 58.580 45.833 2.30 0.00 46.16 3.33
3758 5527 2.410730 CGTAGCCAAACGACTTCGAAAT 59.589 45.455 5.47 0.00 45.68 2.17
3874 5729 5.917545 TTTTACCTTTCTTCCTACCACCT 57.082 39.130 0.00 0.00 0.00 4.00
3896 5754 4.101585 TCATCTAGGCGGTCTGAATGAAAT 59.898 41.667 6.35 0.00 30.14 2.17
3910 5768 3.511477 TGGAGGGAGTAATCATCTAGGC 58.489 50.000 0.00 0.00 0.00 3.93
3913 5771 5.726560 TGGAATGGAGGGAGTAATCATCTA 58.273 41.667 0.00 0.00 0.00 1.98
3918 5776 7.693969 CAATTATGGAATGGAGGGAGTAATC 57.306 40.000 0.00 0.00 0.00 1.75
3942 5800 2.438392 ACTCTCCCCGTTCCATAATTCC 59.562 50.000 0.00 0.00 0.00 3.01
3951 5833 1.172175 AAGACGTACTCTCCCCGTTC 58.828 55.000 0.00 0.00 34.51 3.95
3954 5836 2.636830 TCTTAAGACGTACTCTCCCCG 58.363 52.381 0.00 0.00 0.00 5.73
3957 5839 5.277925 GCACCTATCTTAAGACGTACTCTCC 60.278 48.000 7.48 0.00 0.00 3.71
3966 5848 4.755266 TCCCAAGCACCTATCTTAAGAC 57.245 45.455 7.48 0.00 0.00 3.01
3967 5849 5.191722 ACAATCCCAAGCACCTATCTTAAGA 59.808 40.000 7.82 7.82 0.00 2.10
3968 5850 5.440610 ACAATCCCAAGCACCTATCTTAAG 58.559 41.667 0.00 0.00 0.00 1.85
3969 5851 5.450818 ACAATCCCAAGCACCTATCTTAA 57.549 39.130 0.00 0.00 0.00 1.85
3970 5852 5.437060 GAACAATCCCAAGCACCTATCTTA 58.563 41.667 0.00 0.00 0.00 2.10
3971 5853 4.273318 GAACAATCCCAAGCACCTATCTT 58.727 43.478 0.00 0.00 0.00 2.40
3972 5854 3.682718 CGAACAATCCCAAGCACCTATCT 60.683 47.826 0.00 0.00 0.00 1.98
3973 5855 2.614057 CGAACAATCCCAAGCACCTATC 59.386 50.000 0.00 0.00 0.00 2.08
3984 5866 6.626302 TGGTTATTTTTCATCGAACAATCCC 58.374 36.000 0.00 0.00 0.00 3.85
4013 5895 1.251251 GTGAGCTGCTGGGTGAAATT 58.749 50.000 7.01 0.00 0.00 1.82
4061 5965 6.398918 CAACTACTACTGCTTGTGTTAGGAT 58.601 40.000 0.00 0.00 0.00 3.24
4095 6001 9.921637 TGTTTCGTGATCATGCAACTATATATA 57.078 29.630 24.48 6.25 0.00 0.86
4096 6002 8.831715 TGTTTCGTGATCATGCAACTATATAT 57.168 30.769 24.48 0.00 0.00 0.86
4122 6028 6.632834 TCTCGTAAAACTTCTACGTACAACAC 59.367 38.462 0.00 0.00 42.16 3.32
4124 6030 6.632834 TGTCTCGTAAAACTTCTACGTACAAC 59.367 38.462 0.00 0.00 42.16 3.32
4130 6036 4.619760 TGCATGTCTCGTAAAACTTCTACG 59.380 41.667 0.00 0.00 42.73 3.51
4131 6037 6.462073 TTGCATGTCTCGTAAAACTTCTAC 57.538 37.500 0.00 0.00 0.00 2.59
4132 6038 5.120208 GCTTGCATGTCTCGTAAAACTTCTA 59.880 40.000 1.14 0.00 0.00 2.10
4133 6039 4.083802 GCTTGCATGTCTCGTAAAACTTCT 60.084 41.667 1.14 0.00 0.00 2.85
4149 6055 2.124819 CCTGCTCGAGGCTTGCAT 60.125 61.111 15.58 0.00 42.39 3.96
4168 6074 3.950794 TTGGGCCGCTCATCACGTC 62.951 63.158 0.00 0.00 0.00 4.34
4205 6117 1.985159 AGTCAGGTCCATAAACTGCCA 59.015 47.619 0.00 0.00 32.42 4.92
4221 6133 1.891150 GGGACCAAGTCGAACTAGTCA 59.109 52.381 0.00 0.00 34.88 3.41
4226 6138 0.033090 GAACGGGACCAAGTCGAACT 59.967 55.000 0.00 0.00 32.65 3.01
4386 6325 2.731691 AAGAGACGCAATGCACCGGT 62.732 55.000 0.00 0.00 0.00 5.28
4388 6327 1.133253 CAAGAGACGCAATGCACCG 59.867 57.895 5.91 0.00 0.00 4.94


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.